Wiki

Function

Get ontology term(s) by parent id

Description

ontogetdown finds ontology terms matching a query. All children of the term, related to the term by 'is_a' (class/subclass) relationships, are returned. The information may be written to an output file in various formats.

The default behaviour is to not use or return obsolete terms. This option if set will include all terms.

Boolean value Yes/No

No

Advanced (Unprompted) qualifiers

(none)

Associated qualifiers

"-oboterms" associated obo qualifiers

-iformat1-iformat_oboterms

string

Input obo format

Any string

-idbname1-idbname_oboterms

string

User-provided database name

Any string

"-outfile" associated outobo qualifiers

-odirectory2-odirectory_outfile

string

Output directory

Any string

-oformat2-oformat_outfile

string

Ontology term output format

Any string

General qualifiers

-auto

boolean

Turn off prompts

Boolean value Yes/No

N

-stdout

boolean

Write first file to standard output

Boolean value Yes/No

N

-filter

boolean

Read first file from standard input, write first file to standard output

Boolean value Yes/No

N

-options

boolean

Prompt for standard and additional values

Boolean value Yes/No

N

-debug

boolean

Write debug output to program.dbg

Boolean value Yes/No

N

-verbose

boolean

Report some/full command line options

Boolean value Yes/No

Y

-help

boolean

Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose

Boolean value Yes/No

N

-warning

boolean

Report warnings

Boolean value Yes/No

Y

-error

boolean

Report errors

Boolean value Yes/No

Y

-fatal

boolean

Report fatal errors

Boolean value Yes/No

Y

-die

boolean

Report dying program messages

Boolean value Yes/No

Y

-version

boolean

Report version number and exit

Boolean value Yes/No

N

Input file format

The input is a standard EMBOSS ontology query.

The major ontology sources defined as standard in EMBOSS
installations are EDAM, GO (gene Ontology) and SO (Sequence Ontology).

Data can also be read from ontology output in "obo" format written by an
EMBOSS application.

Input files for usage example

Database entry: edam:0000850

[Term]
id: EDAM:0000850
name: Sequence set
namespace: data
def: A collection of multiple molecular sequences and associated metadata that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method.
comment: This term may be used for arbitrary sequence sets and associated data arising from processing.
subset: data
is_a: EDAM:0002955 ! Sequence report

Output file format

The output is a standard EMBOSS ontology term file.

The results can be output in one of several styles by using the
command-line qualifier -oformat xxx, where 'xxx' is replaced by
the name of the required format. The available format names are: obo,
brief, list, html, xml, json, excel.